The Genome Assembly of Vitis vinifera cv. Shiraz

Figure 3

Repeat structure of V. vinifera Shiraz clone 1654. (a) Genome wide classification of transposable elements (TEs) annotated in the Shiraz primary assembly. LTR, MITE, LINE, RC, and SINE TEs are broken down into subclasses and colored according to their class. (b) Classification of TEs that are annotated 1 kb upstream, downstream, and intronic of an annotated gene or exonic of a Pinot Noir gene/CDS combo. Gaps in Pinot Noir gene/CDS alignments to the Shiraz reference are depicted as dashed lines. (c) TEs that are specific to Shiraz after overlapping genic TEs with structural variants from Nebbiolo, Chardonnay, Carménère, Zinfandel, Cabernet Sauvignon, Sauvignon Blanc, Riesling, and merlot long-read data: (i) upstream, (ii) downstream, (iii) intronic, and (iv) exonic.

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